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MAQC Publishes Results of Large-Scale Comparative Microarray Study, Says Cross-Platform Data Are 'Reproducible and Comparable'

NEW YORK (GenomeWeb News) – Microarray data from different platforms can be “reproducible and comparable,” according to a collection of articles published in Friday's issue of Nature Biotechnology by the Microarray Quality Control Consortium — a community-wide effort to evaluate the reliability of DNA microarray data. 
The MAQC is spearheaded by the US Food and Drug Administration and involves 137 participants representing 51 organizations, including the National Institutes of Health, the US Department of Agriculture, and the Environmental Protection Agency.
The Nature Biotech papers, available here, represent the first formal results of the study to be published.
The project compared multiple whole-genome gene expression profiles across seven commercial platforms. The main study carried out 60 hybridizations on each of the platforms. Around 1,300 microarrays were used during the entire project.
According to a Nature Biotech editorial summarizing the results of the project, the study confirms that “with careful experimental design and appropriate data transformation and analysis, microarray data can indeed be reproducible and comparable among different formats and laboratories, irrespective of sample labeling format.”
The study also found that fold change results from microarray experiments “correlate closely with results from assays like quantitative reverse transcription PCR,” and that variation between microarray runs was “relatively low.”
In an opinion piece accompanying the papers, Janet Woodcock, deputy commissioner for operations at the FDA, and Daniel Casciano of the University of Arkansas for Medical Sciences noted that “a major criticism voiced about microarray studies has been the lack of reproducibility and accuracy of the derived data.”
Woodcock and Casciano added, “It is anticipated that the MAQC project will help improve microarray technology and foster its appropriate application in discovery, development and review of FDA-regulated products."

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